I needed to run a Java program as part of the build process, and the application plugin came with too much baggage.
I did fidde with the application plugin, but in the end I used the much less "invasive" JavaExec plugin.
I have a class file MyObfuscator.class in the build.outputDirectory and before I had a pom.xml like this, which ran code obfuscation in the build directory with two parameters:
<project>
    ...
    <build>
        ...
        <plugins>
            ...
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <version>1.2.1</version>
                <executions>
                    <execution>
                        <id>obfuscate</id>
                        <phase>package</phase>
                        <goals>
                            <goal>exec</goal>
                        </goals>
                        
                        <configuration>
                            <executable>java</executable>
                            <workingDirectory>${project.build.outputDirectory}</workingDirectory>
                            <arguments>
                                <argument>-Djava.library.path=.</argument>
                                <argument>-classpath</argument>
                                <argument>${project.build.outputDirectory}:lib.jar</argument>
                                <argument>MyObfuscator</argument>
                                <argument>HELLO</argument>
                                <argument>GOODBYE</argument>
                            </arguments>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            ...
        </plugins>
    </build>
    ...
</project>
I boiled it down to this thing in Gradle:
apply plugin: "java"
// ...
task obfuscate(type: JavaExec) {
    // Make sure it runs after compilation and resources.
    // Skip this if that's not a requirement.
    dependsOn classes
    
    // run in the buildDir (this requirement was what
    // made a simple "doLast" infeasible)
    workingDir = file(buildDir)
    classpath = files([
        "${buildDir}/classes",
        "${buildDir}/resources/main/lib.jar"
    ])
    main = "MyObfuscator"
}
If you need parameterized execution like in the Maven example above, then add a few lines to the task:
task obfuscate(type: JavaExec) {
    // ... (as above)
    
    // Set PARAM1 to a default value when it's not
    // defined on the command line
    if(!project.hasProperty("PARAM1")) {
        ext.PARAM1 = "HELLO"
    }
    // PARAM1 is dynamic and PARAM2 is static, always "GOODBYE"
    args = [PARAM1, "GOODBYE"]
}
Then depend the assemble task on obfuscate (put this line anywhere below the obfuscate task definition):
assemble.dependsOn obfuscate
Or let the (earlier) jar task depend on it. See the graph at the bottom of this docs section here for more ideas on where to inject this.
You can then call gradle like gradle build -PPARAM1=HELLO to run a parameterized build.